docs: VCell org retrospective (since September 2018)#1715
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WIP checkpoint for the VCell org retrospective (since 2018-09). - Phase 0 data foundation: PR metadata, contributors, releases, READMEs, languages for all 28 in-scope repos; org Project #1 (1,220 items); repo inventories; provenance README. - Phase 1a: catalog.md with code-first summaries for all repos in 7 groups plus a stats table. - HANDOFF.md: full plan/decisions/state so the task can resume autonomously. Remaining: per-repo diff-led timelines (repos/*.md) + synthesis (00-executive-summary, 01-timeline, METHODOLOGY) + draft PR. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Per-repo entries (repos/*.md) for all 28 in-scope repositories, grouped into 15 files. Each is code-first and diff-led per the evidence hierarchy (diffs > releases/tags > README > project board > PR/commit messages): project background, themed-milestone timeline, notable-PRs table, contributors, and tech/stack notes. Direct-commit (0-PR) repos reconstructed from git history. DECISIONS.md records non-trivial scope/grouping choices and the material diff-discovered corrections to the Phase-1a catalog. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Top-level docs synthesized FROM the per-repo entries so summary and detail cannot drift: - 00-executive-summary.md: eras, by-the-numbers, compact catalog, key people - 01-timeline.md: org-wide chronological narrative + key architectural transitions - METHODOLOGY.md: evidence hierarchy, phases, provenance, reproduction - README.md: folder index / reading order Surgical catalog.md corrections from diff-verified findings (staggered ~2-year solver extraction; pyvcell origin 2024-08; vcdb is a published-BioModels data repo; vcell-fenics is an experimental agent-driven sprint). Removed HANDOFF.md (autonomous run complete). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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VCell Org Retrospective (since September 2018)
A comprehensive historical retrospective and feature timeline of Virtual Cell
across the
virtualcellandcam-center(Langevin / SpringSaLaD) GitHub orgs,covering 2018-09-01 → 2026-06. Modeled on the BioSimulations org retrospective.
Everything is code-first / diff-led: diffs, releases, and tags are ground
truth; PRs and the project board are corroborating hints only (VCell adopted a
PR-based workflow only ~2022, so the first four years are reconstructed from
releases/tags/commits).
What's here (
docs/retrospective/)README.md— folder index / reading order.00-executive-summary.md— six eras, by-the-numbers, compact catalog, key people.01-timeline.md— org-wide chronological narrative + key architectural transitions.catalog.md— code-first summary + stats for all 28 repos (7 groups).repos/*.md— 15 detailed, diff-led per-repo entries (the source thetop-level docs are synthesized from, so summary and detail can't drift).
METHODOLOGY.md— evidence hierarchy, phases, provenance, reproduction.DECISIONS.md— non-trivial decisions + diff-discovered catalog corrections (for review).data/— rawgh-pulled provenance snapshots (regenerable).Scope
vcelldominates at 821.openapi-generator,vcell-jsbml, etc.).How it was produced
Phase 0 data foundation → Phase 1a code-first catalog → Phase 1b parallel,
diff-led per-repo research → Phase 2 synthesis. Per-repo research surfaced several
diff-verified corrections to first-pass assumptions (staggered ~2-year solver
extraction;
pyvcellorigin 2024-08;vcdbis a published-BioModels datarepo;
vcell-fenicsis an experimental ~11-day agent-driven sprint;libvcellpackages the Java core via GraalVM native-image; VCell-AI uses OpenAI/Azure) —
all captured in
DECISIONS.mdand folded into the catalog.🤖 Generated with Claude Code